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Yorodumi- PDB-1j2x: Crystal structure of RAP74 C-terminal domain complexed with FCP1 ... -
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-Basic information
Entry | Database: PDB / ID: 1j2x | ||||||
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Title | Crystal structure of RAP74 C-terminal domain complexed with FCP1 C-terminal peptide | ||||||
Components |
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Keywords | TRANSCRIPTION / GENERAL TRANSCRIPTION FACTOR / RAP74 / RAP30 / TFIIF / RNA POLYMERASE II / WINGED-HELIX DOMAIN / FCP1 / CTD / phosphatase | ||||||
Function / homology | Function and homology information RNA polymerase II CTD heptapeptide repeat phosphatase activity / negative regulation of cell growth involved in cardiac muscle cell development / Tat protein binding / phosphatase activator activity / TFIIF-class transcription factor complex binding / transcription factor TFIIF complex / positive regulation by host of viral transcription / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA polymerase II general transcription initiation factor binding / FGFR2 alternative splicing ...RNA polymerase II CTD heptapeptide repeat phosphatase activity / negative regulation of cell growth involved in cardiac muscle cell development / Tat protein binding / phosphatase activator activity / TFIIF-class transcription factor complex binding / transcription factor TFIIF complex / positive regulation by host of viral transcription / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA polymerase II general transcription initiation factor binding / FGFR2 alternative splicing / Signaling by FGFR2 IIIa TM / exit from mitosis / Viral Messenger RNA Synthesis / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / myosin phosphatase activity / mRNA Capping / protein-serine/threonine phosphatase / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / mRNA Splicing - Minor Pathway / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / phosphoprotein phosphatase activity / Processing of Capped Intron-Containing Pre-mRNA / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / spindle midzone / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / protein dephosphorylation / mRNA Splicing - Major Pathway / negative regulation of protein binding / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / promoter-specific chromatin binding / positive regulation of transcription elongation by RNA polymerase II / transcription elongation by RNA polymerase II / response to virus / spindle / spindle pole / cell junction / midbody / protein phosphatase binding / Estrogen-dependent gene expression / transcription by RNA polymerase II / protein domain specific binding / cell division / intracellular membrane-bounded organelle / centrosome / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kamada, K. / Roeder, R.G. / Burley, S.K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Molecular mechanism of recruitment of TFIIF- associating RNA polymerase C-terminal domain phosphatase (FCP1) by transcription factor IIF Authors: Kamada, K. / Roeder, R.G. / Burley, S.K. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Crystal structure of the C-terminal domain of the RAP74 subunit of human transcription factor IIF Authors: Kamada, K. / De Angelis, J. / Roeder, R.G. / Burley, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j2x.cif.gz | 33.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j2x.ent.gz | 20.9 KB | Display | PDB format |
PDBx/mmJSON format | 1j2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j2x_validation.pdf.gz | 446.1 KB | Display | wwPDB validaton report |
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Full document | 1j2x_full_validation.pdf.gz | 447.3 KB | Display | |
Data in XML | 1j2x_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 1j2x_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/1j2x ftp://data.pdbj.org/pub/pdb/validation_reports/j2/1j2x | HTTPS FTP |
-Related structure data
Related structure data | 1i27S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8374.801 Da / Num. of mol.: 1 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAP74 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): UT5600 / References: UniProt: P35269 | ||||
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#2: Protein/peptide | Mass: 1981.183 Da / Num. of mol.: 1 / Fragment: C-terminal peptide / Source method: obtained synthetically / Details: chemical synthesis / References: UniProt: Q9Y5B0 | ||||
#3: Chemical | #4: Chemical | ChemComp-ZN / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 34.86 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEGMME 550, zinc sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.97899 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 18, 2001 / Details: flat cylindrically bent mirror |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97899 Å / Relative weight: 1 |
Reflection | Resolution: 2→22.73 Å / Num. all: 5657 / Num. obs: 5657 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 11 Å2 / Limit h max: 28 / Limit h min: -29 / Limit k max: 15 / Limit k min: -29 / Limit l max: 23 / Limit l min: 0 / Observed criterion F max: 791649.05 / Observed criterion F min: 4.9 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 5.3 / Num. unique all: 271 / Rsym value: 0.164 / % possible all: 97.8 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / Num. measured all: 29692 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1I27 Resolution: 2→22.73 Å / Rfactor Rfree error: 0.013 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 36.4994 Å2 / ksol: 0.378793 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.28 Å2 / Biso mean: 25.29 Å2 / Biso min: 7.16 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→22.73 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 22.7 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.204 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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